This gene encodes a CSL zinc finger-containing protein that is required for dipthamide biosynthesis. The encoded protein is necessary for the initial step in the modification of a histidine residue in elongation factor-2 to diphthamide. This modified residue is a target for ADP ribosylation by the bacterial toxins diphtheria toxin and Pseudomonas exotoxin A. Alternative splicin... See more...

Aliases for DPH3 Gene

Aliases for DPH3 Gene

  • Diphthamide Biosynthesis 3 2 3 5
  • DESR1 2 3 4
  • CSL-Type Zinc Finger-Containing Protein 2 3 4
  • DPH3 Homolog (KTI11, S. Cerevisiae) 2 3
  • Zinc Finger, CSL-Type Containing 2 2 3
  • DelGEF-Interacting Protein 1 3 4
  • DPH3 Homolog 3 4
  • DELGIP1 2 3
  • DELGIP 2 3
  • DPH3A 2 3
  • KTI11 2 3
  • ZCSL2 3 4
  • Deafness Locus Putative Guanine Nucleotide Exchange Factor Interacting Protein 1 3
  • Diphtheria Toxin And Pseudomonas Exotoxin A Sensitivity Required Gene 1 3
  • DPH3A, KTI11 Homolog A (S. Cerevisiae) 2
  • Zinc Finger, CSL Domain Containing 2 3
  • DPH3, KTI11 Homolog (S. Cerevisiae) 2
  • Del-GEF Interacting Protein 3
  • DPH3A, KTI11 Homolog A 3
  • DPH3, KTI11 Homolog 3
  • MGC20197 2
  • DelGIP1 4
  • DPH3 5

External Ids for DPH3 Gene

Previous HGNC Symbols for DPH3 Gene

  • ZCSL2

Previous GeneCards Identifiers for DPH3 Gene

  • GC03M016277
  • GC03M016298

Summaries for DPH3 Gene

Entrez Gene Summary for DPH3 Gene

  • This gene encodes a CSL zinc finger-containing protein that is required for dipthamide biosynthesis. The encoded protein is necessary for the initial step in the modification of a histidine residue in elongation factor-2 to diphthamide. This modified residue is a target for ADP ribosylation by the bacterial toxins diphtheria toxin and Pseudomonas exotoxin A. Alternative splicing results in multiple transcript variants that encode the same isoform. [provided by RefSeq, Feb 2009]

GeneCards Summary for DPH3 Gene

DPH3 (Diphthamide Biosynthesis 3) is a Protein Coding gene. Diseases associated with DPH3 include Diphtheria and Melanoma, Cutaneous Malignant 1. Among its related pathways are Metabolism of proteins and Gamma carboxylation, hypusine formation and arylsulfatase activation.

UniProtKB/Swiss-Prot Summary for DPH3 Gene

  • Essential for the first step in the synthesis of diphthamide, a post-translational modification of histidine which occurs in elongation factor 2 (EEF2) and which can be ADP-ribosylated by diphtheria toxin and by Pseudomonas exotoxin A (Eta).
  • Down-regulation increases extracellular release of proteoglycans, indicating a possible role in the secretion process. Stimulates binding of GNEFR to SEC5.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DPH3 Gene

Genomics for DPH3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for DPH3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DPH3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DPH3

Top Transcription factor binding sites by QIAGEN in the DPH3 gene promoter:
  • AREB6
  • ATF6
  • CREB
  • deltaCREB
  • E2F
  • E2F-1
  • FOXJ2
  • FOXJ2 (long isoform)
  • HTF
  • Pbx1a

Genomic Locations for DPH3 Gene

Genomic Locations for DPH3 Gene
chr3:16,257,061-16,264,969
(GRCh38/hg38)
Size:
7,909 bases
Orientation:
Minus strand
chr3:16,298,568-16,306,496
(GRCh37/hg19)
Size:
7,929 bases
Orientation:
Minus strand

Genomic View for DPH3 Gene

Genes around DPH3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DPH3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DPH3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DPH3 Gene

Proteins for DPH3 Gene

  • Protein details for DPH3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96FX2-DPH3_HUMAN
    Recommended name:
    DPH3 homolog
    Protein Accession:
    Q96FX2

    Protein attributes for DPH3 Gene

    Size:
    82 amino acids
    Molecular mass:
    9240 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for DPH3 Gene

    Alternative splice isoforms for DPH3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DPH3 Gene

Post-translational modifications for DPH3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DPH3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for DPH3 Gene

Domains & Families for DPH3 Gene

Gene Families for DPH3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for DPH3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for DPH3 Gene

GenScript: Design optimal peptide antigens:
  • DelGEF-interacting protein 1 (DPH3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96FX2

UniProtKB/Swiss-Prot:

DPH3_HUMAN :
  • The DPH-type metal-binding (MB) domain can bind either zinc or iron ions.
  • Belongs to the DPH3 family.
Domain:
  • The DPH-type metal-binding (MB) domain can bind either zinc or iron ions.
Family:
  • Belongs to the DPH3 family.
genes like me logo Genes that share domains with DPH3: view

Function for DPH3 Gene

Molecular function for DPH3 Gene

UniProtKB/Swiss-Prot Function:
Essential for the first step in the synthesis of diphthamide, a post-translational modification of histidine which occurs in elongation factor 2 (EEF2) and which can be ADP-ribosylated by diphtheria toxin and by Pseudomonas exotoxin A (Eta).
UniProtKB/Swiss-Prot Function:
Down-regulation increases extracellular release of proteoglycans, indicating a possible role in the secretion process. Stimulates binding of GNEFR to SEC5.

Phenotypes From GWAS Catalog for DPH3 Gene

Gene Ontology (GO) - Molecular Function for DPH3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 14980502
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with DPH3: view
genes like me logo Genes that share phenotypes with DPH3: view

Animal Models for DPH3 Gene

MGI Knock Outs for DPH3:
  • Dph3 Dph3<tm1Lepp>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DPH3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for DPH3 Gene

Localization for DPH3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DPH3 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DPH3 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 2
cytoskeleton 1
mitochondrion 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DPH3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 14980502
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA,IDA 14980502
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with DPH3: view

Pathways & Interactions for DPH3 Gene

genes like me logo Genes that share pathways with DPH3: view

UniProtKB/Swiss-Prot Q96FX2-DPH3_HUMAN

  • Pathway: Protein modification; peptidyl-diphthamide biosynthesis.

Gene Ontology (GO) - Biological Process for DPH3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002098 tRNA wobble uridine modification IBA 21873635
GO:0017183 peptidyl-diphthamide biosynthetic process from peptidyl-histidine TAS --
GO:0050709 negative regulation of protein secretion IDA 14980502
GO:0051099 positive regulation of binding IDA 14980502
genes like me logo Genes that share ontologies with DPH3: view

No data available for SIGNOR curated interactions for DPH3 Gene

Drugs & Compounds for DPH3 Gene

No Compound Related Data Available

Transcripts for DPH3 Gene

mRNA/cDNA for DPH3 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DPH3

Alternative Splicing Database (ASD) splice patterns (SP) for DPH3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d · 4e
SP1: - -
SP2: - -
SP3: -
SP4:
SP5: - - -

Relevant External Links for DPH3 Gene

GeneLoc Exon Structure for
DPH3

Expression for DPH3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for DPH3 Gene

Protein differential expression in normal tissues from HIPED for DPH3 Gene

This gene is overexpressed in Fetal Liver (43.4) and CD4 Tcells (25.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DPH3 Gene



Protein tissue co-expression partners for DPH3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DPH3

SOURCE GeneReport for Unigene cluster for DPH3 Gene:

Hs.388087

mRNA Expression by UniProt/SwissProt for DPH3 Gene:

Q96FX2-DPH3_HUMAN
Tissue specificity: Widely expressed with highest levels in small intestine, spleen, thymus, heart, liver and lung.

Evidence on tissue expression from TISSUES for DPH3 Gene

  • Skin(4.4)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with DPH3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for DPH3 Gene

Orthologs for DPH3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for DPH3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia DPH3 30 31
  • 98.78 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia DPH3 30 31
  • 93.09 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Dph3 30
  • 92.28 (n)
Mouse
(Mus musculus)
Mammalia Dph3 30 17 31
  • 91.06 (n)
OneToMany
Dph3b-ps 31
  • 82 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia DPH3 30 31
  • 90.24 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 82 (a)
OneToMany
-- 31
  • 74 (a)
OneToMany
Chicken
(Gallus gallus)
Aves DPH3 30 31
  • 70.46 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia DPH3 31
  • 78 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia dph3 30
  • 74.8 (n)
Zebrafish
(Danio rerio)
Actinopterygii dph3 30 31
  • 69.7 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG14701 30 31
  • 66.67 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011288 30
  • 61.04 (n)
Worm
(Caenorhabditis elegans)
Secernentea dph-3 30 31
  • 61.9 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes KTI11 31
  • 39 (a)
OneToOne
Species where no ortholog for DPH3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for DPH3 Gene

ENSEMBL:
Gene Tree for DPH3 (if available)
TreeFam:
Gene Tree for DPH3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DPH3: view image

Paralogs for DPH3 Gene

(2) SIMAP similar genes for DPH3 Gene using alignment to 1 proteins:

  • DPH3_HUMAN

Pseudogenes.org Pseudogenes for DPH3 Gene

genes like me logo Genes that share paralogs with DPH3: view

No data available for Paralogs for DPH3 Gene

Variants for DPH3 Gene

Additional dbSNP identifiers (rs#s) for DPH3 Gene

Variation tolerance for DPH3 Gene

Residual Variation Intolerance Score: 54.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.27; 6.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DPH3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DPH3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Structural Variations from Database of Genomic Variants (DGV) for DPH3 Gene

Disorders for DPH3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for DPH3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
diphtheria
  • corynebacterium infection
melanoma, cutaneous malignant 1
  • melanoma, cutaneous malignant, susceptibility to, 1
benign epilepsy with centrotemporal spikes
  • centrotemporal epilepsy
- elite association - COSMIC cancer census association via MalaCards
Search DPH3 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with DPH3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DPH3 Gene

Publications for DPH3 Gene

  1. Characterisation of an evolutionary conserved protein interacting with the putative guanine nucleotide exchange factor DelGEF and modulating secretion. (PMID: 14980502) Sjölinder M … Ponstingl H (Experimental cell research 2004) 2 3 4 23
  2. Retroviral insertional mutagenesis identifies a small protein required for synthesis of diphthamide, the target of bacterial ADP-ribosylating toxins. (PMID: 14527407) Liu S … Leppla SH (Molecular cell 2003) 2 3 4
  3. Solution structure of human DESR1, a CSL zinc-binding protein. (PMID: 18214955) Wu F … Shi Y (Proteins 2008) 3 4
  4. Dph3, a small protein required for diphthamide biosynthesis, is essential in mouse development. (PMID: 16648478) Liu S … Leppla SH (Molecular and cellular biology 2006) 2 3
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for DPH3 Gene

Sources for DPH3 Gene